Renamed all fields to have a consitent naming. Adjusted form for adding new content types to help ensure the wrong term isn't used for creating an entity

tripal/api/tripal.entities.api.inc

@@ -469,6 +469,10 @@ function tripal_set_bundle_variable($variable_name, $bundle_id, $value) {
 
   $variable = tripal_get_variable($variable_name);
 
+  if (!$variable) {
+    return FALSE;
+  }
+
   // And then we need to write the new format to the tripal_bundle_variables table.
   $record = array(
     'bundle_id' => $bundle_id,

tripal/includes/TripalBundleUIController.inc

@@ -98,15 +98,46 @@ function tripal_tripal_bundle_form($form, &$form_state, $entityDataType) {
   );
 
   if ($term) {
+
+    $rows = array(
+      array(
+        array(
+          'header' => TRUE,
+          'data' => 'Vocabulary',
+          'class' => array('side-header')
+        ),
+        $vocab->namespace
+      ),
+      array(
+        array(
+          'header' => TRUE,
+          'data' => 'Term',
+          'class' => array('side-header')
+        ),
+        $term->name
+      ),
+      array(
+        array(
+          'header' => TRUE,
+          'data' => 'Definition',
+          'class' => array('side-header')
+        ),
+        $term->definition
+      )
+    );
+    $table_vars = array(
+      'header' => array(),
+      'rows' => $rows,
+      'attributes' => array(),
+      'caption' => '',
+      'sticky' => FALSE,
+      'colgroups' => array(),
+      'empty' => '',
+    );
     $form['term'] = array(
-      '#type' => 'markup',
-      '#markup' => theme('table', array(
-        'header' => array(),
-        'rows' => array(
-          array(array('header' => TRUE, 'data' => 'Vocabulary', 'class' => array('side-header')), $vocab->namespace),
-          array(array('header' => TRUE, 'data' => 'Term', 'class' => array('side-header')), $term->name),
-        )
-      ))
+      '#type' => 'item',
+      '#title' => t('Vocabulary Term'),
+      '#markup' => theme_table($table_vars)
     );
   }
 

tripal_chado/includes/fields/base__dbxref_id.inc → tripal_chado/includes/fields/chado_base__dbxref_id.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_dbxref_id_formatter(&$element, $entity_type, $entity, $field,
+function chado_base__dbxref_id_formatter(&$element, $entity_type, $entity, $field,
     $instance, $langcode, $items, $display) {
 
   foreach ($items as $delta => $item) {
@@ -42,7 +42,7 @@ function tripal_chado_dbxref_id_formatter(&$element, $entity_type, $entity, $fie
  * @param unknown $delta
  * @param unknown $element
  */
-function tripal_chado_dbxref_id_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
+function chado_base__dbxref_id_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
   $field_name = $field['field_name'];
 
   // Get the field defaults.
@@ -86,8 +86,8 @@ function tripal_chado_dbxref_id_widget(&$widget, $form, $form_state, $field, $in
   $schema = chado_get_schema('dbxref');
   $options = tripal_get_db_select_options();
 
-  $widget['#element_validate'] = array('tripal_chado_dbxref_id_widget_validate');
-  $widget['#theme'] = 'tripal_chado_dbxref_id_widget';
+  $widget['#element_validate'] = array('chado_base__dbxref_id_widget_validate');
+  $widget['#theme'] = 'chado_base__dbxref_id_widget';
   $widget['#prefix'] =  "<span id='$field_name-dbxref--db-id'>";
   $widget['#suffix'] =  "</span>";
 
@@ -96,7 +96,7 @@ function tripal_chado_dbxref_id_widget(&$widget, $form, $form_state, $field, $in
     '#title' => $element['#title'],
     '#description' =>  $element['#description'],
     '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
-    '#theme' => 'tripal_chado_dbxref_id_widget',
+    '#theme' => 'chado_base__dbxref_id_widget',
     //'#collapsible' => TRUE,
     //'#collapsed' => $collapsed,
   );
@@ -113,7 +113,7 @@ function tripal_chado_dbxref_id_widget(&$widget, $form, $form_state, $field, $in
     '#required' => $element['#required'],
     '#default_value' => $db_id,
     '#ajax' => array(
-      'callback' => "tripal_chado_dbxref_id_widget_form_ajax_callback",
+      'callback' => "chado_base__dbxref_id_widget_form_ajax_callback",
       'wrapper' => "$field_name-dbxref--db-id",
       'effect' => 'fade',
       'method' => 'replace'
@@ -158,7 +158,7 @@ function tripal_chado_dbxref_id_widget(&$widget, $form, $form_state, $field, $in
 /**
  * An Ajax callback for the tripal_chado_admin_publish_form..
  */
-function tripal_chado_dbxref_id_widget_form_ajax_callback($form, $form_state) {
+function chado_base__dbxref_id_widget_form_ajax_callback($form, $form_state) {
   $field_name = $form_state['triggering_element']['#parents'][0];
   $db_id = tripal_chado_get_field_form_values($field_name, $form_state, 0, 'dbxref__db_id');
   $accession = tripal_chado_get_field_form_values($field_name, $form_state, 0, 'dbxref__accession');
@@ -180,7 +180,7 @@ function tripal_chado_dbxref_id_widget_form_ajax_callback($form, $form_state) {
 /**
  * Callback function for validating the tripal_chado_organism_select_widget.
  */
-function tripal_chado_dbxref_id_widget_validate($element, &$form_state) {
+function chado_base__dbxref_id_widget_validate($element, &$form_state) {
   $field_name = $element['#parents'][0];
 
   // If the form ID is field_ui_field_edit_form, then the user is editing the
@@ -234,7 +234,7 @@ function tripal_chado_dbxref_id_widget_validate($element, &$form_state) {
  *
  * @param $variables
  */
-function theme_tripal_chado_dbxref_id_widget($variables) {
+function theme_chado_base__dbxref_id_widget($variables) {
   $element = $variables['element'];
 
   $layout = "
@@ -285,7 +285,7 @@ function theme_tripal_chado_dbxref_id_widget($variables) {
  * @param $base_table
  * @param $record
  */
-function tripal_chado_dbxref_id_field_load($field, $entity, $base_table, $record) {
+function chado_base__dbxref_id_field_load($field, $entity, $base_table, $record) {
 
   $field_name = $field['field_name'];
   $field_type = $field['type'];

tripal_chado/includes/fields/base__organism_id.inc → tripal_chado/includes/fields/chado_base__organism_id.inc

@@ -11,7 +11,7 @@
  * @param $display
  * @return string
  */
-function tripal_chado_organism_select_formatter(&$element, $entity_type, $entity, $field,
+function chado_base__organism_id_formatter(&$element, $entity_type, $entity, $field,
     $instance, $langcode, $items, $display) {
 
   foreach ($items as $delta => $item) {
@@ -36,7 +36,7 @@ function tripal_chado_organism_select_formatter(&$element, $entity_type, $entity
  * @param $delta
  * @param $element
  */
-function tripal_chado_organism_select_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
+function chado_base__organism_id_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
   $options = tripal_get_organism_select_options(FALSE);
   $widget['value'] = array(
     '#type' => 'select',
@@ -47,7 +47,7 @@ function tripal_chado_organism_select_widget(&$widget, $form, $form_state, $fiel
     '#required' => $element['#required'],
     '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
     '#delta' => $delta,
-    '#element_validate' => array('tripal_chado_organism_select_widget_validate'),
+    '#element_validate' => array('chado_base__organism_id_widget_validate'),
   );
   $widget['add_organism'] = array(
     '#type' => 'item',
@@ -55,9 +55,9 @@ function tripal_chado_organism_select_widget(&$widget, $form, $form_state, $fiel
   );
 }
 /**
- * Callback function for validating the tripal_chado_organism_select_widget.
+ * Callback function for validating the chado_base__organism_id_widget.
  */
-function tripal_chado_organism_select_widget_validate($element, &$form_state) {
+function chado_base__organism_id_widget_validate($element, &$form_state) {
   $field_name = $element['#parents'][0];
 
   // If the form ID is field_ui_field_edit_form, then the user is editing the
@@ -90,7 +90,7 @@ function tripal_chado_organism_select_widget_validate($element, &$form_state) {
  * @param $form_state
  *   The form state of the (entire) configuration form.
  */
-function tripal_chado_organism_select_formatter_form($field, $instance,
+function chado_base__organism_id_formatter_form($field, $instance,
     $view_mode, $form, &$form_state) {
 
   $display = $instance['display'][$view_mode];

tripal_chado/includes/fields/feature__md5checksum.inc → tripal_chado/includes/fields/chado_feature__md5checksum.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_md5checksum_checkbox_formatter(&$element, $entity_type, $entity, $field,
+function chado_feature__md5checksum_formatter(&$element, $entity_type, $entity, $field,
     $instance, $langcode, $items, $display) {
   foreach ($items as $delta => $item) {
     $content = key_exists('value', $item) ? $item['value'] : '';
@@ -34,7 +34,7 @@ function tripal_chado_md5checksum_checkbox_formatter(&$element, $entity_type, $e
  * @param unknown $delta
  * @param unknown $element
  */
-function tripal_chado_md5checksum_checkbox_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
+function chado_feature__md5checksum_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
 
   $widget['value'] = array(
     '#type' => 'checkbox',
@@ -44,13 +44,13 @@ function tripal_chado_md5checksum_checkbox_widget(&$widget, $form, $form_state,
     '#default_value' => 1,
     '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
     '#delta' => $delta,
-    '#element_validate' => array('tripal_chado_md5checksum_checkbox_widget_validate'),
+    '#element_validate' => array('chado_feature__md5checksum_widget_validate'),
   );
 }
 /**
- * Callback function for validating the tripal_chado_md5checksum_checkbox_widget.
+ * Callback function for validating the chado_feature__md5checksum_widget.
  */
-function tripal_chado_md5checksum_checkbox_widget_validate($element, &$form_state) {
+function chado_feature__md5checksum_widget_validate($element, &$form_state) {
   $field_name = $element['#parents'][0];
 
   // Calculate the md5 checksum for the sequence only if md5 box is checked and
@@ -76,7 +76,7 @@ function tripal_chado_md5checksum_checkbox_widget_validate($element, &$form_stat
  * @param $entity
  * @param $record
  */
-function tripal_chado_md5checksum_field_load($field, $entity, $record) {
+function chado_feature__md5checksum_field_load($field, $entity, $record) {
   $field_name = $field['field_name'];
   if ($record and property_exists($record, 'md5checksum')) {
     $entity->{$field_name}['und'][] = array('value' => $record->md5checksum);

tripal_chado/includes/fields/feature__residues.inc → tripal_chado/includes/fields/chado_feature__residues.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_residues_textarea_formatter(&$element, $entity_type, $entity, $field,
+function chado_feature__residues_formatter(&$element, $entity_type, $entity, $field,
   $instance, $langcode, $items, $display) {
 
   foreach ($items as $delta => $item) {
@@ -37,7 +37,7 @@ function tripal_chado_residues_textarea_formatter(&$element, $entity_type, $enti
  * @param unknown $delta
  * @param unknown $element
  */
-function tripal_chado_residues_textarea_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
+function chado_feature__residues_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
 
   $widget['value'] = array(
     '#type' => 'textarea',
@@ -46,14 +46,14 @@ function tripal_chado_residues_textarea_widget(&$widget, $form, $form_state, $fi
     '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
     '#default_value' => count($items) > 0 ? $items[0]['value'] : '',
     '#delta' => $delta,
-    '#element_validate' => array('tripal_chado_residues_textarea_widget_validate'),
+    '#element_validate' => array('chado_feature__residues_widget_validate'),
     '#cols' => 30,
   );
 }
 /**
- * Callback function for validating the tripal_chado_residues_textarea_widget.
+ * Callback function for validating the chado_feature__residues_widget.
  */
-function tripal_chado_residues_textarea_widget_validate($element, &$form_state) {
+function chado_feature__residues_widget_validate($element, &$form_state) {
   $field_name = $element['#parents'][0];
 
   // Remove any white spaces.

tripal_chado/includes/fields/feature__seqlen.inc → tripal_chado/includes/fields/chado_feature__seqlen.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_seqlen_hidden_formatter(&$element, $entity_type, $entity, $field,
+function chado_feature__seqlen_formatter(&$element, $entity_type, $entity, $field,
     $instance, $langcode, $items, $display) {
 
   foreach ($items as $delta => $item) {
@@ -36,7 +36,7 @@ function tripal_chado_seqlen_hidden_formatter(&$element, $entity_type, $entity,
  * @param unknown $delta
  * @param unknown $element
  */
-function tripal_chado_seqlen_hidden_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
+function chado_feature__seqlen_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
 
   $widget['value'] =  array(
     '#type' => 'hidden',
@@ -44,13 +44,13 @@ function tripal_chado_seqlen_hidden_widget(&$widget, $form, $form_state, $field,
     '#description' => $element['#description'],
     '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
     '#delta' => $delta,
-    '#element_validate' => array('tripal_chado_seqlen_hidden_widget_validate'),
+    '#element_validate' => array('chado_feature__seqlen_widget_validate'),
   );
 }
 /**
- * Callback function for validating the tripal_chado_seqlen_hidden_widget.
+ * Callback function for validating the chado_feature__seqlen_widget.
  */
-function tripal_chado_seqlen_hidden_widget_validate($element, &$form_state) {
+function chado_feature__seqlen_widget_validate($element, &$form_state) {
   $field_name = $element['#parents'][0];
 
   // Get the residues so we can calculate teh length.

tripal_chado/includes/fields/linker_cvterm.inc → tripal_chado/includes/fields/chado_linker__cvterm.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_cvterm_formatter(&$element, $entity_type, $entity, $field,
+function chado_linker__cvterm_formatter(&$element, $entity_type, $entity, $field,
     $instance, $langcode, $items, $display) {
 
   $headers = array('Term', 'Definition', 'Is Not', 'Reference');
@@ -79,7 +79,7 @@ function tripal_chado_cvterm_formatter(&$element, $entity_type, $entity, $field,
  * @param unknown $delta
  * @param unknown $element
  */
-function tripal_chado_cvterm_widget(&$widget, $form, $form_state, $field,
+function chado_linker__cvterm_widget(&$widget, $form, $form_state, $field,
     $instance, $langcode, $items, $delta, $element) {
 
   $entity = $form['#entity'];
@@ -138,8 +138,8 @@ function tripal_chado_cvterm_widget(&$widget, $form, $form_state, $field,
 
   $widget['#table_name'] = $chado_table;
   $widget['#fkey_field'] = $fkey;
-  $widget['#element_validate'] = array('tripal_chado_cvterm_widget_validate');
-  $widget['#theme'] = 'tripal_chado_cvterm_widget';
+  $widget['#element_validate'] = array('chado_linker__cvterm_widget_validate');
+  $widget['#theme'] = 'chado_linker__cvterm_widget';
   $widget['#prefix'] =  "<span id='$table_name-$delta'>";
   $widget['#suffix'] =  "</span>";
 
@@ -168,7 +168,7 @@ function tripal_chado_cvterm_widget(&$widget, $form, $form_state, $field,
     '#maxlength' => array_key_exists('length', $schema['fields']['name']) ? $schema['fields']['name']['length'] : 255,
     '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/cvterm/' . $cv_id,
     '#ajax' => array(
-      'callback' => "tripal_chado_cvterm_widget_form_ajax_callback",
+      'callback' => "chado_linker__cvterm_widget_form_ajax_callback",
       'wrapper' => "$table_name-$delta",
       'effect' => 'fade',
       'method' => 'replace'
@@ -191,7 +191,7 @@ function tripal_chado_cvterm_widget(&$widget, $form, $form_state, $field,
 /**
  * An Ajax callback for the dbxref widget.
  */
-function tripal_chado_cvterm_widget_form_ajax_callback($form, $form_state) {
+function chado_linker__cvterm_widget_form_ajax_callback($form, $form_state) {
 
   $field_name = $form_state['triggering_element']['#parents'][0];
   $delta = $form_state['triggering_element']['#parents'][2];
@@ -203,7 +203,7 @@ function tripal_chado_cvterm_widget_form_ajax_callback($form, $form_state) {
 /**
  * Callback function for validating the tripal_chado_organism_select_widget.
  */
-function tripal_chado_cvterm_widget_validate($element, &$form_state) {
+function chado_linker__cvterm_widget_validate($element, &$form_state) {
 
   $field_name = $element['#field_name'];
   $delta = $element['#delta'];
@@ -254,7 +254,7 @@ function tripal_chado_cvterm_widget_validate($element, &$form_state) {
  *
  * @param $variables
  */
-function theme_tripal_chado_cvterm_widget($variables) {
+function theme_chado_linker__cvterm_widget($variables) {
   $element = $variables['element'];
 
   // These two fields were added to the widget to help identify the fields
@@ -292,7 +292,7 @@ function theme_tripal_chado_cvterm_widget($variables) {
  * @param $base_table
  * @param $record
  */
-function tripal_chado_cvterm_field_load($field, $entity, $base_table, $record) {
+function chado_linker__cvterm_load($field, $entity, $base_table, $record) {
 
   $field_name = $field['field_name'];
   $field_type = $field['type'];

tripal_chado/includes/fields/linker_cvterm_adder.inc → tripal_chado/includes/fields/chado_linker__cvterm_adder.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_cvterm_class_adder_formatter(&$element, $entity_type, $entity, $field,
+function chado_linker__cvterm_adder_formatter(&$element, $entity_type, $entity, $field,
   $instance, $langcode, $items, $display) {
 
   foreach ($items as $delta => $item) {
@@ -20,12 +20,12 @@ function tripal_chado_cvterm_class_adder_formatter(&$element, $entity_type, $ent
 /**
  *
  */
-function tripal_chado_cvterm_class_adder_widget(&$widget, &$form, &$form_state,
+function chado_linker__cvterm_adder_widget(&$widget, &$form, &$form_state,
     $field, $instance, $langcode, $items, $delta, $element) {
 
   // This field has no value field.  Just a fieldset for adding new annotation types.
 
-  $widget['#element_validate'] = array('tripal_chado_cvterm_class_adder_widget_validate');
+  $widget['#element_validate'] = array('chado_linker__cvterm_adder_widget_validate');
 
   $widget['#type'] = 'fieldset';
   $widget['#title'] = $element['#title'];
@@ -62,14 +62,14 @@ function tripal_chado_cvterm_class_adder_widget(&$widget, &$form, &$form_state,
     '#value' => t('Add Annotation Type'),
     '#type' => 'submit',
     '#name' => 'cvterm_class_adder_button',
-    '#submit' => array('tripal_chado_cvterm_class_adder_widget_submit'),
+    '#submit' => array('chado_linker__cvterm_adder_widget_submit'),
     '#limit_validation_errors' => array(array($field['field_name'])),
   );
 }
 /**
- * Callback function for validating the tripal_chado_cvterm_class_adder_widget.
+ * Callback function for validating the chado_linker__cvterm_adder_widget.
  */
-function tripal_chado_cvterm_class_adder_widget_validate($element, &$form_state) {
+function chado_linker__cvterm_adder_widget_validate($element, &$form_state) {
 
    // Add the new field to the entity
    if (array_key_exists('triggering_element', $form_state) and
@@ -121,8 +121,8 @@ function tripal_chado_cvterm_class_adder_widget_validate($element, &$form_state)
    }
 }
 /**
- * Callback function for submitting the tripal_chado_cvterm_class_adder_widget.
+ * Callback function for submitting the chado_linker__cvterm_adder_widget.
  */
-function tripal_chado_cvterm_class_adder_widget_submit($element, &$form_state) {
+function chado_linker__cvterm_adder_widget_submit($element, &$form_state) {
 
 }

tripal_chado/includes/fields/linker_dbxref.inc → tripal_chado/includes/fields/chado_linker__dbxref.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_dbxref_formatter(&$element, $entity_type, $entity, $field,
+function chado_linker__dbxref_formatter(&$element, $entity_type, $entity, $field,
     $instance, $langcode, $items, $display) {
 
   $chado_table = $field['settings']['chado_table'];
@@ -42,7 +42,7 @@ function tripal_chado_dbxref_formatter(&$element, $entity_type, $entity, $field,
  * @param unknown $delta
  * @param unknown $element
  */
-function tripal_chado_dbxref_widget(&$widget, $form, $form_state, $field,
+function chado_linker__dbxref_widget(&$widget, $form, $form_state, $field,
     $instance, $langcode, $items, $delta, $element) {
 
   $field_name = $field['field_name'];
@@ -92,8 +92,8 @@ function tripal_chado_dbxref_widget(&$widget, $form, $form_state, $field,
 
   $widget['#table_name'] = $chado_table;
   $widget['#fkey_field'] = $fkey;
-  $widget['#element_validate'] = array('tripal_chado_dbxref_widget_validate');
-  $widget['#theme'] = 'tripal_chado_dbxref_widget';
+  $widget['#element_validate'] = array('chado_linker__dbxref_widget_validate');
+  $widget['#theme'] = 'chado_linker__dbxref_widget';
   $widget['#prefix'] =  "<span id='$field_name-dbxref--db-id-$delta'>";
   $widget['#suffix'] =  "</span>";
 
@@ -120,7 +120,7 @@ function tripal_chado_dbxref_widget(&$widget, $form, $form_state, $field,
     '#required' => $element['#required'],
     '#default_value' => $db_id,
     '#ajax' => array(
-      'callback' => "tripal_chado_dbxref_widget_form_ajax_callback",
+      'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
       'wrapper' => "$field_name-dbxref--db-id-$delta",
       'effect' => 'fade',
       'method' => 'replace'
@@ -135,7 +135,7 @@ function tripal_chado_dbxref_widget(&$widget, $form, $form_state, $field,
     '#size' => 15,
     '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/dbxref/' . $db_id,
     '#ajax' => array(
-      'callback' => "tripal_chado_dbxref_widget_form_ajax_callback",
+      'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
       'wrapper' => "$field_name-dbxref--db-id-$delta",
       'effect' => 'fade',
       'method' => 'replace'
@@ -167,7 +167,7 @@ function tripal_chado_dbxref_widget(&$widget, $form, $form_state, $field,
 /**
  * An Ajax callback for the dbxref widget.
  */
-function tripal_chado_dbxref_widget_form_ajax_callback($form, $form_state) {
+function chado_linker__dbxref_widget_form_ajax_callback($form, $form_state) {
 
   $field_name = $form_state['triggering_element']['#parents'][0];
   $delta = $form_state['triggering_element']['#parents'][2];
@@ -194,7 +194,7 @@ function tripal_chado_dbxref_widget_form_ajax_callback($form, $form_state) {
 /**
  * Callback function for validating the tripal_chado_organism_select_widget.
  */
-function tripal_chado_dbxref_widget_validate($element, &$form_state) {
+function chado_linker__dbxref_widget_validate($element, &$form_state) {
 
   $field_name = $element['#field_name'];
   $delta = $element['#delta'];
@@ -256,7 +256,7 @@ function tripal_chado_dbxref_widget_validate($element, &$form_state) {
  *
  * @param $variables
  */
-function theme_tripal_chado_dbxref_widget($variables) {
+function theme_chado_linker__dbxref_widget($variables) {
   $element = $variables['element'];
 
   // These two fields were added to the widget to help identify the fields
@@ -298,7 +298,7 @@ function theme_tripal_chado_dbxref_widget($variables) {
  * @param $base_table
  * @param $record
  */
-function tripal_chado_dbxref_field_load($field, $entity, $base_table, $record) {
+function chado_linker__dbxref_load($field, $entity, $base_table, $record) {
 
   $field_name = $field['field_name'];
   $field_type = $field['type'];

tripal_chado/includes/fields/linker_prop.inc → tripal_chado/includes/fields/chado_linker__prop.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_kvproperty_formatter(&$element, $entity_type, $entity, $field,
+function chado_linker__prop_formatter(&$element, $entity_type, $entity, $field,
   $instance, $langcode, $items, $display) {
 
   $field_name = $field['field_name'];
@@ -39,7 +39,7 @@ function tripal_chado_kvproperty_formatter(&$element, $entity_type, $entity, $fi
  * @param unknown $delta
  * @param unknown $element
  */
-function tripal_chado_kvproperty_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
+function chado_linker__prop_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
   $entity = $form['#entity'];
   $field_name = $field['field_name'];
 
@@ -84,7 +84,7 @@ function tripal_chado_kvproperty_widget(&$widget, $form, $form_state, $field, $i
   $widget['#field_name'] = $element['#field_name'];
   $widget['#language'] = $element['#language'];
   $widget['#weight'] = isset($element['#weight']) ? $element['#weight'] : 0;
-  $widget['#element_validate'] = array('tripal_chado_kvproperty_widget_validate');
+  $widget['#element_validate'] = array('chado_linker__prop_widget_validate');
   $widget['#cardinality'] = 1;
 
   $widget['value'] = array(
@@ -115,14 +115,14 @@ function tripal_chado_kvproperty_widget(&$widget, $form, $form_state, $field, $i
  * @param unknown $form
  * @param unknown $form_state
  */
-function tripal_chado_kvproperty_widget_form_ajax_callback($form, $form_state) {
+function chado_linker__prop_widget_form_ajax_callback($form, $form_state) {
   $field_name = $form_state['triggering_element']['#parents'][0];
   return $form[$field_name];
 }
 /**
- * Callback function for validating the tripal_chado_kvproperty_widget.
+ * Callback function for validating the chado_linker__prop_widget.
  */
-function tripal_chado_kvproperty_widget_validate($element, &$form_state) {
+function chado_linker__prop_widget_validate($element, &$form_state) {
   $field_name = $element['#field_name'];
   $delta = $element['#delta'];
   $entity = $element['#entity'];
@@ -172,9 +172,9 @@ function tripal_chado_kvproperty_widget_validate($element, &$form_state) {
   }
 }
 /**
- * Callback function for submitting the tripal_chado_kvproperty_widget.
+ * Callback function for submitting the chado_linker__prop_widget.
  */
-function tripal_chado_kvproperty_widget_submit($element, &$form_state) {
+function chado_linker__prop_widget_submit($element, &$form_state) {
 }
 
 /**
@@ -190,7 +190,7 @@ function tripal_chado_kvproperty_widget_submit($element, &$form_state) {
  * @param $base_table
  * @param $record
  */
-function tripal_chado_kvproperty_field_load($field, $entity, $base_table, $record) {
+function chado_linker__prop_load($field, $entity, $base_table, $record) {
 
   $field_name = $field['field_name'];
   $field_type = $field['type'];

tripal_chado/includes/fields/linker_prop_adder.inc → tripal_chado/includes/fields/chado_linker__prop_adder.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_kvproperty_adder_formatter(&$element, $entity_type, $entity, $field,
+function chado_linker__prop_adder_formatter(&$element, $entity_type, $entity, $field,
   $instance, $langcode, $items, $display) {
 
   foreach ($items as $delta => $item) {
@@ -20,10 +20,10 @@ function tripal_chado_kvproperty_adder_formatter(&$element, $entity_type, $entit
 /**
  *
  */
-function tripal_chado_kvproperty_adder_widget(&$widget, $form, $form_state,
+function chado_linker__prop_adder_widget(&$widget, $form, $form_state,
     $field, $instance, $langcode, $items, $delta, $element) {
   // This field has no value field.  Just a fieldset for adding new properties.
-  $widget['#element_validate'] = array('tripal_chado_kvproperty_adder_widget_validate');
+  $widget['#element_validate'] = array('chado_linker__prop_adder_widget_validate');
 
   $widget['#type'] = 'fieldset';
   $widget['#title'] = $element['#title'];
@@ -61,14 +61,14 @@ function tripal_chado_kvproperty_adder_widget(&$widget, $form, $form_state,
     '#value' => t('Add Property'),
     '#type' => 'submit',
     '#name' => 'kvproperty_adder_button',
-    '#submit' => array('tripal_chado_kvproperty_adder_widget_submit'),
+    '#submit' => array('chado_linker__prop_adder_widget_submit'),
     '#limit_validation_errors' => array(array($field['field_name'])),
   );
 }
 /**
- * Callback function for validating the tripal_chado_kvproperty_adder_widget.
+ * Callback function for validating the chado_linker__prop_adder_widget.
  */
-function tripal_chado_kvproperty_adder_widget_validate($element, &$form_state) {
+function chado_linker__prop_adder_widget_validate($element, &$form_state) {
 
    // Add the new field to the entity
    if (array_key_exists('triggering_element', $form_state) and
@@ -122,7 +122,7 @@ function tripal_chado_kvproperty_adder_widget_validate($element, &$form_state) {
    }
 }
 /**
- * Callback function for submitting the tripal_chado_kvproperty_adder_widget.
+ * Callback function for submitting the chado_linker__prop_adder_widget.
  */
-function tripal_chado_kvproperty_adder_widget_submit($element, &$form_state) {
+function chado_linker__prop_adder_widget_submit($element, &$form_state) {
 }

tripal_chado/includes/fields/base__pub_id.inc → tripal_chado/includes/fields/chado_linker__pub.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_pub_formatter(&$element, $entity_type, $entity, $field,
+function chado_linker__pub_formatter(&$element, $entity_type, $entity, $field,
     $instance, $langcode, $items, $display) {
 
   $list_items = array();
@@ -48,7 +48,7 @@ function tripal_chado_pub_formatter(&$element, $entity_type, $entity, $field,
  * @param unknown $delta
  * @param unknown $element
  */
-function tripal_chado_pub_widget(&$widget, $form, $form_state, $field,
+function chado_linker__pub_widget(&$widget, $form, $form_state, $field,
     $instance, $langcode, $items, $delta, $element) {
 
   $entity = $form['#entity'];
@@ -89,8 +89,8 @@ function tripal_chado_pub_widget(&$widget, $form, $form_state, $field,
 
   $widget['#table_name'] = $table_name;
   $widget['#fkey_field'] = $fkey;
-  $widget['#element_validate'] = array('tripal_chado_pub_widget_validate');
-  $widget['#theme'] = 'tripal_chado_pub_widget';
+  $widget['#element_validate'] = array('chado_linker__pub_widget_validate');
+  $widget['#theme'] = 'chado_linker__pub_widget';
   $widget['#prefix'] =  "<span id='$table_name-$delta'>";
   $widget['#suffix'] =  "</span>";
 
@@ -113,7 +113,7 @@ function tripal_chado_pub_widget(&$widget, $form, $form_state, $field,
     '#default_value' => $title,
     '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/pub',
     '#ajax' => array(
-      'callback' => "tripal_chado_pub_widget_form_ajax_callback",
+      'callback' => "chado_linker__pub_widget_form_ajax_callback",
       'wrapper' => "$table_name-$delta",
       'effect' => 'fade',
       'method' => 'replace'
@@ -124,7 +124,7 @@ function tripal_chado_pub_widget(&$widget, $form, $form_state, $field,
 /**
  * An Ajax callback for the pub widget.
  */
-function tripal_chado_pub_widget_form_ajax_callback($form, $form_state) {
+function chado_linker__pub_widget_form_ajax_callback($form, $form_state) {
 
   $field_name = $form_state['triggering_element']['#parents'][0];
   $delta = $form_state['triggering_element']['#parents'][2];
@@ -135,7 +135,7 @@ function tripal_chado_pub_widget_form_ajax_callback($form, $form_state) {
 /**
  * Callback function for validating the tripal_chado_organism_select_widget.
  */
-function tripal_chado_pub_widget_validate($element, &$form_state) {
+function chado_linker__pub_widget_validate($element, &$form_state) {
 
   $field_name = $element['#field_name'];
   $delta = $element['#delta'];
@@ -181,7 +181,7 @@ function tripal_chado_pub_widget_validate($element, &$form_state) {
  *
  * @param $variables
  */
-function theme_tripal_chado_pub_widget($variables) {
+function theme_chado_linker__pub_widget($variables) {
   $element = $variables['element'];
 
   // These two fields were added to the widget to help identify the fields
@@ -213,7 +213,7 @@ function theme_tripal_chado_pub_widget($variables) {
  * @param $base_table
  * @param $record
  */
-function tripal_chado_pub_field_load($field, $entity, $base_table, $record) {
+function chado_linker__pub_load($field, $entity, $base_table, $record) {
 
   $field_name = $field['field_name'];
   $field_type = $field['type'];

tripal_chado/includes/fields/linker_synonym.inc → tripal_chado/includes/fields/chado_linker__synonym.inc

@@ -10,7 +10,7 @@
  * @param unknown $items
  * @param unknown $display
  */
-function tripal_chado_synonym_formatter(&$element, $entity_type, $entity, $field,
+function chado_linker__synonym_formatter(&$element, $entity_type, $entity, $field,
     $instance, $langcode, $items, $display) {
 
   $chado_table = $field['settings']['chado_table'];
@@ -41,7 +41,7 @@ function tripal_chado_synonym_formatter(&$element, $entity_type, $entity, $field
  * @param unknown $delta
  * @param unknown $element
  */
-function tripal_chado_synonym_widget(&$widget, $form, $form_state, $field,
+function chado_linker__synonym_widget(&$widget, $form, $form_state, $field,
     $instance, $langcode, $items, $delta, $element) {
 
   $entity = $form['#entity'];
@@ -100,8 +100,8 @@ function tripal_chado_synonym_widget(&$widget, $form, $form_state, $field,
 
   $widget['#table_name'] = $table_name;
   $widget['#fkey_field'] = $fkey;
-  $widget['#element_validate'] = array('tripal_chado_synonym_widget_validate');
-  $widget['#theme'] = 'tripal_chado_synonym_widget';
+  $widget['#element_validate'] = array('chado_linker__synonym_widget_validate');
+  $widget['#theme'] = 'chado_linker__synonym_widget';
   $widget['#prefix'] =  "<span id='$table_name-$delta'>";
   $widget['#suffix'] =  "</span>";
 
@@ -145,7 +145,7 @@ function tripal_chado_synonym_widget(&$widget, $form, $form_state, $field,
 /**
  * An Ajax callback for the synonym widget.
  */
-function tripal_chado_synonym_widget_form_ajax_callback($form, $form_state) {
+function chado_linker__synonym_widget_form_ajax_callback($form, $form_state) {
 
   $field_name = $form_state['triggering_element']['#parents'][0];
   $delta = $form_state['triggering_element']['#parents'][2];
@@ -156,7 +156,7 @@ function tripal_chado_synonym_widget_form_ajax_callback($form, $form_state) {
 /**
  * Callback function for validating the tripal_chado_organism_select_widget.
  */
-function tripal_chado_synonym_widget_validate($element, &$form_state) {
+function chado_linker__synonym_widget_validate($element, &$form_state) {
 
   $field_name = $element['#field_name'];
   $delta = $element['#delta'];
@@ -229,7 +229,7 @@ function tripal_chado_synonym_widget_validate($element, &$form_state) {
  *
  * @param $variables
  */
-function theme_tripal_chado_synonym_widget($variables) {
+function theme_chado_linker__synonym_widget($variables) {
   $element = $variables['element'];
 
   // These two fields were added to the widget to help identify the fields
@@ -270,7 +270,7 @@ function theme_tripal_chado_synonym_widget($variables) {
  * @param $base_table
  * @param $record
  */
-function tripal_chado_synonym_field_load($field, $entity, $base_table, $record) {
+function chado_linker__synonym_load($field, $entity, $base_table, $record) {
 
   $field_name = $field['field_name'];
   $field_type = $field['type'];

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -325,7 +325,7 @@ function tripal_chado_field_storage_load($entity_type, $entities, $age,
         // Allow the creating module to alter the value if desired.  The
         // module should do this if the field has any other form elements
         // that need populationg besides the default value.
-        $load_function = $field_module . '_' . $field_type . '_field_load';
+        $load_function = $field_type . '_load';
         module_load_include('inc', $field_module, 'includes/fields/' . $field_type);
         if (function_exists($load_function)) {
           $load_function($field, $entity, $base_table, $record);
@@ -338,7 +338,7 @@ function tripal_chado_field_storage_load($entity_type, $entities, $age,
       if ($field_table != $base_table) {
         // Set an empty value by default, and let the hook function update it.
         $entity->{$field_name}['und'][0]['value'] = '';
-        $load_function = $field_module . '_' . $field_type . '_field_load';
+        $load_function = $field_type . '_load';
         module_load_include('inc', $field_module, 'includes/fields/' . $field_type);
         if (function_exists($load_function)) {
           $load_function($field, $entity, $base_table, $record);

tripal_chado/includes/tripal_chado.fields.inc

@@ -11,8 +11,8 @@ function tripal_chado_field_info() {
     'chado_base__organism_id' => array(
       'label' => t('Organism'),
       'description' => t('A field for specifying an organism.'),
-      'default_widget' => 'tripal_chado_organism_select_widget',
-      'default_formatter' => 'tripal_chado_organism_formatter',
+      'default_widget' => 'chado_base__organism_id_widget',
+      'default_formatter' => 'chado_base__organism_id_formatter',
       'settings' => array(),
       'storage' => array(
         'type' => 'field_chado_storage',
@@ -20,26 +20,14 @@ function tripal_chado_field_info() {
         'active' => TRUE
       ),
     ),
+
     'chado_base__dbxref_id' => array(
       'label' => t('Cross reference'),
       'description' => t('This record can be cross referenced with a record in
           another online database. This field is intended for the most prominent
           reference.  At a minimum, the database and accession must be provided.'),
-      'default_widget' => 'tripal_chado_dbxref_id_widget',
-      'default_formatter' => 'tripal_chado_dbxref_id_formatter',
-      'settings' => array(),
-      'storage' => array(
-        'type' => 'field_chado_storage',
-        'module' => 'tripal_chado',
-        'active' => TRUE
-      ),
-    ),
-    'chado_base_pub_id' => array(
-      'label' => t('Publications'),
-      'description' => t('Associates a publication (e.g. journal article,
-          conference proceedings, book chapter, etc.) with this record.'),
-      'default_widget' => 'tripal_chado_pub_widget',
-      'default_formatter' => 'tripal_chado_pub_formatter',
+      'default_widget' => 'chado_base__dbxref_id_widget',
+      'default_formatter' => 'chado_base__dbxref_id_formatter',
       'settings' => array(),
       'storage' => array(
         'type' => 'field_chado_storage',
@@ -51,12 +39,12 @@ function tripal_chado_field_info() {
     /*
      * Fields that support linker tables.
      */
-    'chado_linker_cvterm' => array(
+    'chado_linker__cvterm' => array(
       'label' => t('Annotations'),
       'description' => t('This record can be annotated with terms
           from other vocabularies.'),
-      'default_widget' => 'tripal_chado_cvterm_widget',
-      'default_formatter' => 'tripal_chado_cvterm_formatter',
+      'default_widget' => 'chado_linker__cvterm_widget',
+      'default_formatter' => 'chado_linker__cvterm_formatter',
       'settings' => array(),
       'storage' => array(
         'type' => 'field_chado_storage',
@@ -64,11 +52,11 @@ function tripal_chado_field_info() {
         'active' => TRUE
       ),
     ),
-    'chado_linker_synonym' => array(
+    'chado_linker__synonym' => array(
       'label' => t('Synonyms'),
       'description' => t('Adds an alternative name (synonym or alias) to this record.'),
-      'default_widget' => 'tripal_chado_synonym_widget',
-      'default_formatter' => 'tripal_chado_synonym_formatter',
+      'default_widget' => 'chado_linker__synonym_widget',
+      'default_formatter' => 'chado_linker__synonym_formatter',
       'settings' => array(),
       'storage' => array(
         'type' => 'field_chado_storage',
@@ -76,11 +64,11 @@ function tripal_chado_field_info() {
         'active' => TRUE
       ),
     ),
-    'chado_linker_prop' => array(
+    'chado_linker__prop' => array(
       'label' => t('Add a Property'),
       'description' => t('Add details about this property.'),
-      'default_widget' => 'tripal_chado_kvproperty_widget',
-      'default_formatter' => 'tripal_chado_kvproperty_formatter',
+      'default_widget' => 'chado_linker__prop_widget',
+      'default_formatter' => 'chado_linker__prop_formatter',
       'settings' => array(),
       'storage' => array(
         'type' => 'field_chado_storage',
@@ -88,13 +76,26 @@ function tripal_chado_field_info() {
         'active' => TRUE
       ),
     ),
-    'chado_linker_dbxref' => array(
+    'chado_linker__dbxref' => array(
       'label' => t('Cross references'),
       'description' => t('This record can be cross referenced with a record in
         another online database. This field is intended for one or more
         references.  At a minimum, the database and accession must be provided.'),
-      'default_widget' => 'tripal_chado_dbxref_widget',
-      'default_formatter' => 'tripal_chado_dbxref_formatter',
+      'default_widget' => 'chado_linker__dbxref_widget',
+      'default_formatter' => 'chado_linker__dbxref_formatter',
+      'settings' => array(),
+      'storage' => array(
+        'type' => 'field_chado_storage',
+        'module' => 'tripal_chado',
+        'active' => TRUE
+      ),
+    ),
+    'chado_linker__pub' => array(
+      'label' => t('Publications'),
+      'description' => t('Associates a publication (e.g. journal article,
+          conference proceedings, book chapter, etc.) with this record.'),
+      'default_widget' => 'chado_linker__pub_widget',
+      'default_formatter' => 'chado_linker__pub_formatter',
       'settings' => array(),
       'storage' => array(
         'type' => 'field_chado_storage',
@@ -107,11 +108,11 @@ function tripal_chado_field_info() {
      * pages.  They are avaiable to site curators when adding/updating
      * a record and allow the user to add new linker table fields.
      */
-    'chado_linker_prop_adder' => array(
+    'chado_linker__prop_adder' => array(
       'label' => t('Add a Property Type'),
       'description' => t('This record may have any number of properties. Use
           this field to first add the type.'),
-      'default_widget' => 'tripal_chado_kvproperty_adder_widget',
+      'default_widget' => 'chado_linker__prop_adder_widget',
       'default_formatter' => 'hidden',
       'settings' => array(),
       'storage' => array(
@@ -124,11 +125,11 @@ function tripal_chado_field_info() {
     // The field provides a widget for adding new vocabularies for cvterm
     // linker tables. This will allow cvterms to be grouped by vocabulary
     // ('category').
-    'chado_linker_cvterm_adder' => array(
+    'chado_linker__cvterm_adder' => array(
       'label' => t('Add an Annotation Type'),
       'description' => t('This record may have any number of types of
           annotations. Use this field to first add the type.'),
-      'default_widget' => 'tripal_chado_cvterm_class_adder_widget',
+      'default_widget' => 'chado_linker__cvterm_adder_widget',
       'default_formatter' => 'hidden',
       'settings' => array(),
       'storage' => array(
@@ -143,8 +144,8 @@ function tripal_chado_field_info() {
     'chado_feature__residues' => array(
       'label' => t('Residues'),
       'description' => t('A field for managing nucleotide and protein residues.'),
-      'default_widget' => 'tripal_chado_residue_textarea_widget',
-      'default_formatter' => 'tripal_chado_residues_formatter',
+      'default_widget' => 'chado_feature__residues_widget',
+      'default_formatter' => 'chado_feature__residues_formatter',
       'settings' => array(),
       'storage' => array(
         'type' => 'field_chado_storage',
@@ -155,8 +156,8 @@ function tripal_chado_field_info() {
     'chado_feature__md5checksum' => array(
       'label' => t('MD5 checksum'),
       'description' => t('A field for generating MD5 checksum for a sequence.'),
-      'default_widget' => 'tripal_chado_md5checksum_checkbox_widget',
-      'default_formatter' => 'tripal_chado_md5checksum_formatter',
+      'default_widget' => 'chado_feature__md5checksum_widget',
+      'default_formatter' => 'chado_feature__md5checksum_formatter',
       'settings' => array(),
       'storage' => array(
         'type' => 'field_chado_storage',
@@ -167,8 +168,8 @@ function tripal_chado_field_info() {
     'chado_feature__seqlen' => array(
       'label' => t('Sequence length'),
       'description' => t('A field for calculating the length of a sequence.'),
-      'default_widget' => 'tripal_chado_seqlen_hidden_widget',
-      'default_formatter' => 'tripal_chado_seqlen_formatter',
+      'default_widget' => 'chado_feature__seqlen_widget',
+      'default_formatter' => 'chado_feature__seqlen_formatter',
       'settings' => array(),
       'storage' => array(
         'type' => 'field_chado_storage',
@@ -180,187 +181,6 @@ function tripal_chado_field_info() {
   );
   return $fields;
 }
-
-/**
- * Implements hook_field_formatter_settings_summary.
- */
-function tripal_chado_field_formatter_settings_summary($field, $instance, $view_mode) {
-
-  $summary = '';
-  switch ($field['type']) {
-    case 'organism_id':
-      $summary = 'Organisms can be displayed in vaious ways.';
-      break;
-    default:
-      $summary = '';
-  }
-
-  return $summary;
-}
-
-/**
- * Implements hook_field_formatter_settings_form.
- */
-function tripal_chado_field_formatter_settings_form($field, $instance, $view_mode, $form, &$form_state) {
-  $element = array();
-  switch ($field['type']) {
-    case 'chado_base__organism_id':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/organism_id');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/organism_id');
-      $element = tripal_chado_organism_select_formatter_form($field, $instance, $view_mode, $form, $form_state);
-      break;
-  }
-
-  return $element;
-}
-
-/**
- * Implements hook_field_formatter_view().
- */
-function tripal_chado_field_formatter_view($entity_type, $entity, $field,
-    $instance, $langcode, $items, $display) {
-
-  $element = array();
-  switch ($display['type']) {
-    case 'chado_base__organism_id_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/organism_id');
-      tripal_chado_organism_select_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_base__dbxref_id_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref_id');
-      tripal_chado_dbxref_id_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_base__pub_id_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/pub');
-      tripal_chado_pub_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_linker_dbxref_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref');
-      tripal_chado_dbxref_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_linker_cvterm_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/cvterm');
-      tripal_chado_cvterm_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_linker_prop_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty');
-      tripal_chado_kvproperty_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_linker_synonym_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/synonym');
-      tripal_chado_synonym_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_linker_prop_adder_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty_adder');
-      tripal_chado_kvproperty_adder_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_linker_cvterm_adder_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/cvterm_class_adder');
-      tripal_chado_cvterm_class_adder_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_feature__md5checksum_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/md5checksum');
-      tripal_chado_md5checksum_checkbox_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_feature__residues_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/residues');
-      tripal_chado_residues_textarea_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-    case 'chado_feature__seqlen_formatter':
-      module_load_include('inc', 'tripal_chado', 'includes/fields/seqlen');
-      tripal_chado_seqlen_hidden_formatter($element, $entity_type, $entity, $field,
-          $instance, $langcode, $items, $display);
-      break;
-
-
-  }
-  return $element;
-}
-
-/**
- * Implements hook_field_widget_form().
- */
-function tripal_chado_field_widget_form(&$form, &$form_state, $field,
-    $instance, $langcode, $items, $delta, $element) {
-
-  $widget = $element;
-  switch ($instance['widget']['type']) {
-    case 'chado_organism_select_widget':
-      // Make sure the include files get parsed now and for the form submits.
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/organism_id');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/organism_id');
-      // Update the widget with the new field.
-      tripal_chado_organism_select_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_dbxref_id_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/dbxref_id');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref_id');
-      tripal_chado_dbxref_id_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_dbxref_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/dbxref');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref');
-      tripal_chado_dbxref_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_cvterm_class_adder_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/cvterm_class_adder');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/cvterm_class_adder');
-      tripal_chado_cvterm_class_adder_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_cvterm_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/cvterm');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/cvterm');
-      tripal_chado_cvterm_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_md5checksum_checkbox_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/md5checksum');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/md5checksum');
-      tripal_chado_md5checksum_checkbox_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_residues_textarea_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/residues');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/residues');
-      tripal_chado_residues_textarea_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_seqlen_hidden_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/seqlen');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/seqlen');
-      tripal_chado_seqlen_hidden_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_kvproperty_adder_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/kvproperty_adder');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty_adder');
-      tripal_chado_kvproperty_adder_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_kvproperty_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/kvproperty');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty');
-      tripal_chado_kvproperty_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_synonym_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/synonym');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/synonym');
-      tripal_chado_synonym_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-    case 'chado_pub_widget':
-      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/pub');
-      module_load_include('inc', 'tripal_chado', 'includes/fields/pub');
-      tripal_chado_pub_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
-      break;
-  }
-  return $widget;
-}
 /**
  * Implements hook_field_widget_info().
  */
@@ -368,79 +188,209 @@ function tripal_chado_field_widget_info() {
   return array(
     /*
      * Generic fields that support multiple base tables.
-     */
+  */
     'chado_base__organism_id_widget' => array(
       'label' => t('Organism Select'),
-      'field types' => array('organism_id')
+      'field types' => array('chado_base__organism_id')
     ),
     'chado_base__dbxref_id_widget' => array(
       'label' => t('Cross reference'),
-      'field types' => array('dbxref_id'),
+      'field types' => array('chado_base__dbxref_id'),
       'description' => t('This record can be cross referenced with a record in
         another online database. This field is intended for the most
         prominent reference.  At a minimum, the database and accession
         must be provided.'),
     ),
-    'chado_base__pub_id_widget' => array(
-      'label' => t('Publications'),
-      'field types' => array('pub'),
-    ),
+
     /*
      * Fields that support linker tables.
      */
-    'chado_linker_dbxref_widget' => array(
+    'chado_linker__pub_widget' => array(
+      'label' => t('Publications'),
+      'field types' => array('chado_linker__pub'),
+    ),
+    'chado_linker__dbxref_widget' => array(
       'label' => t('Cross references'),
-      'field types' => array('dbxref'),
+      'field types' => array('chado_linker__dbxref'),
       'description' => t('This record can be cross referenced with a record
         in another online database. This field is intended for the most
         prominent reference.  At a minimum, the database and accession
         must be provided.'),
     ),
 
-    'chado_linker_cvterm_widget' => array(
+    'chado_linker__cvterm_widget' => array(
       'label' => t('Annotations'),
-      'field types' => array('cvterm'),
+      'field types' => array('chado_linker__cvterm'),
       'description' => t('This record can be annotated with terms
           from other vocabularies.'),
     ),
-    'chado_linker_prop_widget' => array(
+    'chado_linker__prop_widget' => array(
       'label' => t('Property'),
-      'field types' => array('kvproperty'),
+      'field types' => array('chado_linker__prop'),
     ),
-    'chado_linker_synonym_widget' => array(
+    'chado_linker__synonym_widget' => array(
       'label' => t('Synonyms'),
-      'field types' => array('synonym'),
+      'field types' => array('chado_linker__synonym'),
     ),
     /*
      * Fields that add new fields. These fields are not shown on
      * pages.  They are avaiable to site curators when adding/updating
      * a record and allow the user to add new linker table fields.
      */
-    'chado_linker_prop_adder_widget' => array(
+    'chado_linker__prop_adder_widget' => array(
       'label' => t('Add a Property'),
-      'field types' => array('kvproperty_adder'),
+      'field types' => array('chado_linker__prop_adder'),
     ),
-    'chado_linker_cvterm_adder_widget' => array(
+    'chado_linker__cvterm_adder_widget' => array(
       'label' => t('Add an Annotation'),
-      'field types' => array('cvterm_class_adder'),
+      'field types' => array('chado_linker__cvterm_adder'),
     ),
     /*
      * Field specific to the feature table of Chado.
      */
     'chado_feature__md5checksum_widget' => array(
       'label' => t('MD5 Checksum Checkbox'),
-      'field types' => array('md5checksum'),
+      'field types' => array('chado_feature__md5checksum'),
     ),
     'chado_feature__residues_widget' => array(
       'label' => t('Residues'),
-      'field types' => array('residues'),
+      'field types' => array('chado_feature__residues'),
     ),
     'chado_feature__seqlen_widget' => array(
       'label' => t('Sequence Length'),
-      'field types' => array('seqlen'),
+      'field types' => array('chado_feature__seqlen'),
     ),
   );
 }
+/**
+ * Implements hook_field_formatter_info().
+ */
+function tripal_chado_field_formatter_info() {
+  return array(
+    'chado_base__organism_id_formatter' => array(
+      'label' => t('Organism'),
+      'field types' => array('chado_base__organism_id')
+    ),
+    'chado_base__dbxref_id_formatter' => array(
+      'label' => t('Cross reference'),
+      'field types' => array('chado_base__dbxref_id')
+    ),
+    'chado_linker__pub_formatter' => array(
+      'label' => t('Publications'),
+      'field types' => array('chado_linker__pub')
+    ),
+    'chado_linker__dbxref_formatter' => array(
+      'label' => t('Cross references'),
+      'field types' => array('chado_linker__dbxref')
+    ),
+    'chado_linker__cvterm_formatter' => array(
+      'label' => t('Annotations'),
+      'field types' => array('chado_linker__cvterm')
+    ),
+    'chado_linker__prop_formatter' => array(
+      'label' => t('Property'),
+      'field types' => array('chado_linker__prop')
+    ),
+    'chado_linker__synonym_formatter' => array(
+      'label' => t('Synonyms'),
+      'field types' => array('chado_linker__synonym')
+    ),
+
+    'chado_linker__cvterm_adder_formatter' => array(
+      'label' => t('Add an Annotation'),
+      'field types' => array('chado_linker__cvterm_adder')
+    ),
+
+    'chado_linker__prop_adder_formatter' => array(
+      'label' => t('Add a Property'),
+      'field types' => array('chado_linker__prop_adder')
+    ),
+
+    'chado_feature__md5checksum_formatter' => array(
+      'label' => t('MD5 checksum'),
+      'field types' => array('chado_feature__md5checksum')
+    ),
+    'chado_feature__residues_formatter' => array(
+      'label' => t('Residues'),
+      'field types' => array('chado_feature__residues')
+    ),
+    'chado_feature__seqlen_formatter' => array(
+      'label' => t('Sequence length'),
+      'field types' => array('chado_feature__seqlen')
+    ),
+  );
+}
+/**
+ * Implements hook_field_formatter_settings_summary.
+ */
+function tripal_chado_field_formatter_settings_summary($field, $instance, $view_mode) {
+
+  $summary = '';
+  switch ($field['type']) {
+    case 'organism_id':
+      $summary = 'Organisms can be displayed in vaious ways.';
+      break;
+    default:
+      $summary = '';
+  }
+
+  return $summary;
+}
+
+/**
+ * Implements hook_field_formatter_settings_form.
+ */
+function tripal_chado_field_formatter_settings_form($field, $instance, $view_mode, $form, &$form_state) {
+  $element = array();
+
+  $field_type = $field['type'];
+  form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/' . $field_type);
+  module_load_include('inc', 'tripal_chado', 'includes/fields/' . $field_type);
+  $function = $field_type . '_formatter_form';
+  if (function_exists($function)) {
+    $element = $function($field, $instance, $view_mode, $form, $form_state);
+  }
+
+  return $element;
+}
+
+/**
+ * Implements hook_field_formatter_view().
+ */
+function tripal_chado_field_formatter_view($entity_type, $entity, $field,
+    $instance, $langcode, $items, $display) {
+
+  $element = array();
+
+  $field_type = $display['type'];
+  module_load_include('inc', 'tripal_chado', 'includes/fields/' . $field_type);
+  $function = $field_type;
+  if (function_exists($function)) {
+    $function($element, $entity_type, $entity, $field, $instance, $langcode, $items, $display);
+  }
+
+  return $element;
+}
+
+/**
+ * Implements hook_field_widget_form().
+ */
+function tripal_chado_field_widget_form(&$form, &$form_state, $field,
+    $instance, $langcode, $items, $delta, $element) {
+
+  $widget = $element;
+
+  $field_type = $instance['widget']['type'];
+  form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/' . $field_type);
+  module_load_include('inc', 'tripal_chado', 'includes/fields/' . $field_type);
+  $function = $field_type;
+  if (function_exists($function)) {
+    $function($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
+  }
+
+  return $widget;
+}
+
 /**
  * Returns the values of the field from the $form_state.
  */
@@ -531,72 +481,13 @@ function tripal_chado_field_widget_form_alter(&$element, &$form_state, $context)
   }
 }
 
-/**
- * Implements hook_field_formatter_info().
- */
-function tripal_chado_field_formatter_info() {
-  return array(
-    'chado_base__organism_id_formatter' => array(
-      'label' => t('Organism'),
-      'field types' => array('organism_id')
-    ),
-    'chado_base__dbxref_id_formatter' => array(
-      'label' => t('Cross reference'),
-      'field types' => array('dbxref_id')
-    ),
-    'chado_base__pub_id_formatter' => array(
-      'label' => t('Publications'),
-      'field types' => array('pub')
-    ),
-
-
-    'chado_linker_dbxref_formatter' => array(
-      'label' => t('Cross references'),
-      'field types' => array('dbxref')
-    ),
-    'chado_linker_cvterm_formatter' => array(
-      'label' => t('Annotations'),
-      'field types' => array('cvterm')
-    ),
-    'chado_linker_prop_formatter' => array(
-      'label' => t('Property'),
-      'field types' => array('kvproperty')
-    ),
-    'chado_linker_synonym_formatter' => array(
-      'label' => t('Synonyms'),
-      'field types' => array('synonym')
-    ),
-
-    'chado_linker_cvterm_adder_formatter' => array(
-      'label' => t('Add an Annotation'),
-      'field types' => array('cvterm_class_adder')
-    ),
 
-    'chado_linker_prop_adder_formatter' => array(
-      'label' => t('Add a Property'),
-      'field types' => array('kvproperty_adder')
-    ),
-
-    'chado_feature__md5checksum_formatter' => array(
-      'label' => t('MD5 checksum'),
-      'field types' => array('md5checksum')
-    ),
-    'chado_feature__residues_formatter' => array(
-      'label' => t('Residues'),
-      'field types' => array('residues')
-    ),
-    'chado_feature__seqlen_formatter' => array(
-      'label' => t('Sequence length'),
-      'field types' => array('seqlen')
-    ),
-  );
-}
 
 /**
  * Returns a $field_info array for a field based on a database column.
  *
  */
-function tripal_chado_add_bundle_fields_base_fields_defaults($table_name, $schema, $column_name) {
+function tripal_chado_add_bundle_fields_base__fields_defaults($table_name, $schema, $column_name) {
   $details = $schema['fields'][$column_name];
 
   // Create an array with information about this field.
@@ -704,7 +595,7 @@ function tripal_chado_add_bundle_fields_base_fields_defaults($table_name, $schem
   //
   if ($field['field_settings']['chado_column'] == 'organism_id') {
     $field['field_type'] = 'chado_base__organism_id';
-    $field['widget_type'] = 'tripal_chado_organism_select_widget';
+    $field['widget_type'] = 'chado_base__organism_id_widget';
     $field['label'] = 'Organism';
     $field['description'] = 'Select an organism.';
     $field['field_settings']['semantic_web']['type'] = 'organism';
@@ -714,7 +605,7 @@ function tripal_chado_add_bundle_fields_base_fields_defaults($table_name, $schem
   }
   elseif ($field['field_settings']['chado_column'] =='dbxref_id') {
     $field['field_type'] = 'chado_base__dbxref_id';
-    $field['widget_type'] = 'tripal_chado_primary_dbxref_widget';
+    $field['widget_type'] = 'chado_base_dbxref_id_widget';
     $field['label'] = 'Cross Reference';
     $field['description'] = 'This record can be cross referenced with a ' .
         'record in another online database. The primary reference is for the ' .
@@ -969,7 +860,7 @@ function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {
   // Adds the fields for the base table to the entity.  Adds fields
   // for all columns including FK fields.  Excludes primary key and the
   // type_id field (that's inherent in the bundle).
-  tripal_chado_add_bundle_fields_base_fields($entity_type, $bundle_name, $bundle_data);
+  tripal_chado_add_bundle_fields_base__fields($entity_type, $bundle_name, $bundle_data);
 
   ////
   //
@@ -979,7 +870,7 @@ function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {
   // base table. If so, add the fields for that type of table.
   $prop_table = $bundle_data['data_table'] . 'prop';
   if (chado_table_exists($prop_table)) {
-    tripal_chado_add_bundle_fields_kvproperty_adder_field($entity_type, $bundle_name, $prop_table, $bundle_data['data_table']);
+    tripal_chado_add_bundle_fields_linker__prop_adder_field($entity_type, $bundle_name, $prop_table, $bundle_data['data_table']);
   }
 
   ////
@@ -990,7 +881,7 @@ function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {
   // base table. If so, add the fields for that type of table.
   $dbxref_table = $bundle_data['data_table'] . '_dbxref';
   if (chado_table_exists($dbxref_table)) {
-    tripal_chado_add_bundle_fields_dbxref_field($entity_type, $bundle_name, $dbxref_table, $bundle_data['data_table']);
+    tripal_chado_add_bundle_fields_linker__dbxref_field($entity_type, $bundle_name, $dbxref_table, $bundle_data['data_table']);
   }
 
   ////
@@ -1001,7 +892,7 @@ function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {
   // base table. If so, add the fields for that type of table.
   $cvterm_table = $bundle_data['data_table'] . '_cvterm';
   if (chado_table_exists($cvterm_table)) {
-    tripal_chado_add_bundle_fields_cvterm_class_adder_field($entity_type, $bundle_name, $cvterm_table, $bundle_data['data_table']);
+    tripal_chado_add_bundle_fields_linker__cvterm_adder_field($entity_type, $bundle_name, $cvterm_table, $bundle_data['data_table']);
   }
 
 
@@ -1013,7 +904,7 @@ function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {
   // base table. If so, add the fields for that type of table.
   $syn_table = $bundle_data['data_table'] . '_synonym';
   if (chado_table_exists($syn_table)) {
-    tripal_chado_add_bundle_fields_synonym_field($entity_type, $bundle_name, $syn_table, $bundle_data['data_table']);
+    tripal_chado_add_bundle_fields_linker__synonym_field($entity_type, $bundle_name, $syn_table, $bundle_data['data_table']);
   }
 
   ////
@@ -1024,7 +915,7 @@ function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {
   // base table. If so, add the fields for that type of table.
   $pub_table = $bundle_data['data_table'] . '_pub';
   if (chado_table_exists($pub_table)) {
-    tripal_chado_add_bundle_fields_pub_field($entity_type, $bundle_name, $pub_table, $bundle_data['data_table']);
+    tripal_chado_add_bundle_fields_linker__pub_field($entity_type, $bundle_name, $pub_table, $bundle_data['data_table']);
   }
 }
 
@@ -1036,7 +927,7 @@ function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {
  * @param $base_table
  * @param $dbxref_table
  */
-function tripal_chado_add_bundle_fields_dbxref_field($entity_type_name, $bundle_name, $dbxref_table, $base_table) {
+function tripal_chado_add_bundle_fields_linker__dbxref_field($entity_type_name, $bundle_name, $dbxref_table, $base_table) {
   // We already have a dbxref_id field.
   $field_name = $dbxref_table;
   $schema = chado_get_schema($dbxref_table);
@@ -1044,8 +935,8 @@ function tripal_chado_add_bundle_fields_dbxref_field($entity_type_name, $bundle_
 
   // Initialize the field array.
   $field_info = array(
-    'field_type' => 'chado_linker_dbxref_adder',
-    'widget_type' => 'chado_linker_dbxref_adder_widget',
+    'field_type' => 'chado_base__dbxref_id',
+    'widget_type' => 'chado_base__dbxref_id_widget',
     'widget_settings' => array('display_label' => 1),
     'description' => '',
     'label' => 'Cross References',
@@ -1087,7 +978,7 @@ function tripal_chado_add_bundle_fields_dbxref_field($entity_type_name, $bundle_
  * @param $base_table
  * @param $dbxref_table
  */
-function tripal_chado_add_bundle_fields_synonym_field($entity_type_name, $bundle_name, $syn_table, $base_table) {
+function tripal_chado_add_bundle_fields_linker__synonym_field($entity_type_name, $bundle_name, $syn_table, $base_table) {
   // We already have a dbxref_id field.
   $field_name = $syn_table;
   $schema = chado_get_schema($syn_table);
@@ -1095,8 +986,8 @@ function tripal_chado_add_bundle_fields_synonym_field($entity_type_name, $bundle
 
   // Initialize the field array.
   $field_info = array(
-    'field_type' => 'chado_linker_synonym',
-    'widget_type' => 'chado_linker_synonym_widget',
+    'field_type' => 'chado_linker__synonym',
+    'widget_type' => 'chado_linker__synonym_widget',
     'widget_settings' => array('display_label' => 1),
     'description' => '',
     'label' => 'Synonyms',
@@ -1132,7 +1023,7 @@ function tripal_chado_add_bundle_fields_synonym_field($entity_type_name, $bundle
  * @param $base_table
  * @param $dbxref_table
  */
-function tripal_chado_add_bundle_fields_pub_field($entity_type_name, $bundle_name, $pub_table, $base_table) {
+function tripal_chado_add_bundle_fields_linker__pub_field($entity_type_name, $bundle_name, $pub_table, $base_table) {
   // We already have a dbxref_id field.
   $field_name = $pub_table;
   $schema = chado_get_schema($pub_table);
@@ -1140,8 +1031,8 @@ function tripal_chado_add_bundle_fields_pub_field($entity_type_name, $bundle_nam
 
   // Initialize the field array.
   $field_info = array(
-    'field_type' => 'chado_base__pub_id',
-    'widget_type' => 'chado_base__pub_id_widget',
+    'field_type' => 'chado_linker__pub',
+    'widget_type' => 'chado_linker__pub_widget',
     'widget_settings' => array('display_label' => 1),
     'description' => '',
     'label' => 'Publications',
@@ -1176,13 +1067,13 @@ function tripal_chado_add_bundle_fields_pub_field($entity_type_name, $bundle_nam
  * @param $bundle_name
  * @param $kv_table
  */
-function tripal_chado_add_bundle_fields_kvproperty_adder_field($entity_type_name, $bundle_name, $kv_table, $base_table) {
+function tripal_chado_add_bundle_fields_linker__prop_adder_field($entity_type_name, $bundle_name, $kv_table, $base_table) {
   $field_name = $kv_table;
 
   // Initialize the field array.
   $field_info = array(
-    'field_type' => 'chado_linker_prop_adder',
-    'widget_type' => 'chado_linker_prop_adder_widget',
+    'field_type' => 'chado_linker__prop_adder',
+    'widget_type' => 'chado_linker__prop_adder_widget',
     'field_settings' => array(
       'base_table' => $base_table,
     ),
@@ -1201,14 +1092,14 @@ function tripal_chado_add_bundle_fields_kvproperty_adder_field($entity_type_name
  * @param $bundle_name
  * @param $kv_table
  */
-function tripal_chado_add_bundle_fields_cvterm_class_adder_field($entity_type_name, $bundle_name, $cvterm_table, $base_table) {
+function tripal_chado_add_bundle_fields_linker__cvterm_adder_field($entity_type_name, $bundle_name, $cvterm_table, $base_table) {
   // First add a generic property field so that users can add new property types.
   $field_name = $cvterm_table;
 
   // Initialize the field array.
   $field_info = array(
-    'field_type' => 'chado_linker_cvterm_adder',
-    'widget_type' => 'chado_linker_cvterm_adder_widget',
+    'field_type' => 'chado_linker__cvterm_adder',
+    'widget_type' => 'chado_linker__cvterm_adder_widget',
     'field_settings' => array(
       'base_table' => $base_table,
     ),
@@ -1223,7 +1114,7 @@ function tripal_chado_add_bundle_fields_cvterm_class_adder_field($entity_type_na
 /**
  * Adds the fields for the base table to the entity.
  */
-function tripal_chado_add_bundle_fields_base_fields($entity_type_name, $bundle_name, $bundle_data) {
+function tripal_chado_add_bundle_fields_base__fields($entity_type_name, $bundle_name, $bundle_data) {
 
   $table_name = $bundle_data['data_table'];
   $type_table = $bundle_data['type_table'];
@@ -1247,7 +1138,7 @@ function tripal_chado_add_bundle_fields_base_fields($entity_type_name, $bundle_n
     }
 
     // Get the field defaults for this column.
-    $field_info = tripal_chado_add_bundle_fields_base_fields_defaults($table_name, $schema, $column_name);
+    $field_info = tripal_chado_add_bundle_fields_base__fields_defaults($table_name, $schema, $column_name);
 
 
     // TODO: add in a call to drupal_alter to allow other modules to change

tripal_chado/includes/tripal_chado.term_storage.inc

@@ -93,60 +93,72 @@ function tripal_chado_vocab_import_form_submit($form, &$form_state) {
  * Implements hook_vocab_select_term_form().
  */
 function tripal_chado_vocab_select_term_form($form, &$form_state) {
-  $term_name = '';
-  $num_terms = 0;
-  $cv_id = '';
-  $terms = array();
-
-  // Set defaults using the form state.
-  if (array_key_exists('storage', $form_state)) {
-    if (array_key_exists('terms', $form_state['storage'])) {
-      $terms = $form_state['storage']['terms'];
-    }
-  }
-  $num_terms = count($terms);
+  $term_name = array_key_exists('values', $form_state) ? $form_state['values']['term_name'] : '';
 
   // If no term has been selected yet then provide the auto complete field.
-  if ($num_terms == 0) {
-    $form['term_name'] = array(
-      '#title'       => t('Content Type'),
-      '#type'        => 'textfield',
-      '#description' => t("The content type must be the name of a term in
-          a controlled vocabulary and the controlled vocabulary should
-          already be loaded into Tripal.  For example, to create a content
-          type for storing 'genes', use the 'gene' term from the
-          Sequence Ontology (SO)."),
-      '#required'    => TRUE,
-      '#default_value' => $term_name,
-      '#autocomplete_path' => "admin/tripal/storage/term/$cv_id",
-    );
-  }
+  $form['term_name'] = array(
+    '#title'       => t('Content Type'),
+    '#type'        => 'textfield',
+    '#description' => t("The content type must be the name of a term in
+        a controlled vocabulary and the controlled vocabulary should
+        already be loaded into Tripal.  For example, to create a content
+        type for storing 'genes', use the 'gene' term from the
+        Sequence Ontology (SO)."),
+    '#required'    => TRUE,
+    '#default_value' => $term_name,
+    '#autocomplete_path' => "admin/tripal/storage/term/",
+  );
+  $form['select_button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Lookup Term'),
+    '#name' => 'select_cvterm',
+    '#ajax' => array(
+      'callback' => "tripal_chado_vocab_select_term_form_ajax_callback",
+      'wrapper' => "tripal-chado-vocab-select-form",
+      'effect' => 'fade',
+      'method' => 'replace'
+    ),
+  );
 
-  // If the term belongs to more than one vocabulary then add additional fields
-  // to let the user select the vocabulary.
-  if ($num_terms > 1) {
-    $form['term_name'] = array(
-      '#type' => 'hidden',
-      '#value' => $term_name,
+  if ($term_name) {
+    $form['terms_list'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Matching Terms'),
+      '#description' => t('Please select the term the best matches the
+          content type you want to create. If the same term exists in
+          multiple vocabularies you will see more than one option below.')
     );
-
-    $cvs = array();
+    $match = array(
+      'name' => $term_name,
+    );
+    $terms = chado_generate_var('cvterm', $match, array('return_array' => TRUE));
+    $terms = chado_expand_var($terms, 'field', 'cvterm.definition');
     foreach ($terms as $term) {
-      $cvs[$term->cv_id->cv_id] = 'Vocabulary: <b>' . $term->cv_id->name . '</b> (' . $term->cv_id->definition . ')<br>' . $term->name . ': ' . $term->definition;
+       $form['terms_list']['term-' . $term->cvterm_id] = array(
+         '#type' => 'checkbox',
+         '#title' =>  $term->name,
+         '#description' => '<b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
+             '<br><b>Definition:</b>  ' . $term->definition,
+       );
     }
-    $form['cv_id'] = array(
-      '#type' => 'radios',
-      '#title' => t('Select the appropriate vocabulary'),
-      '#options' => $cvs,
+    // Add in the button for the cases of no terms or too many.
+    $form['submit_button'] = array(
+      '#type' => 'submit',
+      '#value' => t('Use this term'),
+      '#name' => 'use_cvterm'
     );
   }
 
-  // Add in the button for the cases of no terms or too many.
-  $form['select_button'] = array(
-    '#type' => 'submit',
-    '#value' => t('Use this term'),
-    '#name' => 'select_cvterm'
-  );
+  $form['#prefix'] = '<div id = "tripal-chado-vocab-select-form">';
+  $form['#suffix'] = '</div>';
+
+  return $form;
+}
+
+/**
+ * Implements an AJAX callback for the tripal_chado_vocab_select_term_form.
+ */
+function tripal_chado_vocab_select_term_form_ajax_callback($form, $form_state) {
   return $form;
 }
 
@@ -154,53 +166,38 @@ function tripal_chado_vocab_select_term_form($form, &$form_state) {
  * Implements hook_vocab_select_term_form_validate().
  */
 function tripal_chado_vocab_select_term_form_validate($form, &$form_state) {
+
   if (array_key_exists('clicked_button', $form_state) and
-      $form_state['clicked_button']['#name'] =='select_cvterm') {
+      $form_state['clicked_button']['#name'] =='use_cvterm') {
 
-    // First, make sure the term is unique. If not then we can't check it.
-    $term_name = NULL;
-    $cv_id = NULL;
-    $cvterm = NULL;
-    if (array_key_exists('term_name', $form_state['values'])) {
-      $term_name = $form_state['input']['term_name'];
-    }
-    if (array_key_exists('cv_id', $form_state['input'])) {
-      $cv_id = $form_state['input']['cv_id'];
-    }
+    $cvterm_id = NULL;
 
-    // If a term and $cv_id are provided then we can look for the term using
-    // both and we should find a unique term. If only ther term is provided
-    // we can still look for a unique term but there must only be one.
-    if ($term_name and !$cv_id) {
-      $match = array(
-        'name' => $term_name,
-      );
+    // Make sure we have a cvterm selected
+    $num_selected = 0;
+    foreach ($form_state['values'] as $key => $value) {
+      $matches = array();
+      if (preg_match("/^term-(\d+)$/", $key, $matches) and
+          $form_state['values']['term-' . $matches[1]]) {
+        $cvterm_id = $matches[1];
+        $term = chado_generate_var('cvterm', array('cvterm_id' => $cvterm_id));
+        $num_selected++;
+      }
     }
-    else {
-      $match = array(
-        'name' => $term_name,
-        'cv_id' => $cv_id,
-      );
+    if ($num_selected == 0) {
+      form_set_error('', 'Please select at least one term.');
     }
-    $terms = chado_generate_var('cvterm', $match, array('return_array' => TRUE));
-    $form_state['storage']['terms'] = $terms;
-
-    // If we do not have any terms then the term provided by the user does not
-    // exists and we need to provide an error message.
-    if (count($terms) == 0) {
-      form_set_error('term_name', t('The term does not exist in this database.'));
+    else if ($num_selected > 1) {
+      form_set_error('term-' . $cvterm_id, 'Please select only one term from the list below.');
     }
-    // If we have more than one term then we need to set an error so that the
-    // form can provide a list of vocabularies to select from.
-    if (count($terms) > 1) {
-      form_set_error('term_name', t('The term is not unique. A list of vocabularies
-        that contain this term. Please select the most appropriate vocabulary.'));
-    }
-    // If we have a unique term then set the namespace, accession and name.
-    if (count($terms) == 1) {
-      $form_state['storage']['namespace'] = $terms[0]->dbxref_id->db_id->name;
-      $form_state['storage']['accession'] = $terms[0]->dbxref_id->accession;
-      $form_state['storage']['term_name'] = $terms[0]->name;
+    else {
+      $form_state['storage']['namespace'] = $term->dbxref_id->db_id->name;
+      $form_state['storage']['accession'] = $term->dbxref_id->accession;
+      $form_state['storage']['term_name'] = $term->name;
     }
   }
+  // For any other button click it's an AJAX call and we just want to reubild
+  // the form.
+  else {
+    $form_state['rebuild'] = TRUE;
+  }
 }

tripal_chado/tripal_chado.module

@@ -506,27 +506,27 @@ function tripal_chado_theme($existing, $type, $theme, $path) {
     // Theme fields.
     'chado_base__dbxref_id_widget' => array(
       'render element' => 'element',
-      'file' => 'includes/fields/base__dbxref_id.inc',
+      'file' => 'includes/fields/chado_base__dbxref_id.inc',
     ),
-    'chado_linker_dbxref_widget' => array(
+    'chado_linker__dbxref_widget' => array(
       'render element' => 'element',
-      'file' => 'includes/fields/linker_dbxref.inc',
+      'file' => 'includes/fields/chado_linker__dbxref.inc',
     ),
-    'chado_linker_cvterm_widget' => array(
+    'chado_linker__cvterm_widget' => array(
       'render element' => 'element',
-      'file' => 'includes/fields/cvterm.inc',
+      'file' => 'includes/fields/chado_linker__cvterm.inc',
     ),
-    'chado_linker_synonym_widget' => array(
+    'chado_linker__synonym_widget' => array(
       'render element' => 'element',
-      'file' => 'includes/fields/synonym.inc',
+      'file' => 'includes/fields/chado_linker__synonym.inc',
     ),
-    'chado_base__pub_id_widget' => array(
+    'chado_linker__pub_widget' => array(
       'render element' => 'element',
-      'file' => 'includes/fields/pub.inc',
+      'file' => 'includes/fields/chado_linker__pub.inc',
     ),
-    'chado_linker_prop_adder_widget' => array(
+    'chado_linker__prop_adder_widget' => array(
       'render element' => 'element',
-      'file' => 'includes/fields/dbxref_id.inc',
+      'file' => 'includes/fields/chado_linker__prop_adder.inc',
     ),
     'tripal_chado_date_combo' => array(
       'render element' => 'element',